Minimally invasive capsule-string device enables spatially resolved microbiome profiling across the upper...

Area of Science:

• Microbiology
• Gastroenterology
• Biotechnology

Background:

• Characterizing regional variation in the human gastrointestinal microbiome is challenging due to limitations of current sampling methods like endoscopy or stool analysis.
• Existing techniques fail to accurately represent the upper gastrointestinal tract's microbial composition.

Purpose of the Study:

• To evaluate a novel, minimally invasive capsule-string device for collecting luminal and mucosal samples from the esophagus, stomach, duodenum, and jejunum.
• To assess the feasibility and effectiveness of this device in characterizing upper gastrointestinal microbiota.

Main Methods:

• A capsule-string device was used for natural transit sampling in healthy adults.
• Samples were anatomically localized using pH, bile staining, and string length.
• Microbial communities were profiled using 16S rRNA gene sequencing.

Main Results:

• The device was well-tolerated and successfully recovered sufficient microbial biomass from all targeted upper GI regions.
• Distinct microbial signatures were identified across different compartments, particularly between proximal (esophageal/gastric) and small intestinal communities.
• Host-specific variations were dominant, yet a reproducible regional microbial signal was consistently observed.

Conclusions:

• Capsule-string sampling offers a reliable, non-endoscopic method for obtaining spatially resolved upper gastrointestinal microbiota.
• This technique provides unprecedented access to historically inaccessible regions, enabling precise mapping of in vivo gut microbial organization.
• The approach opens new avenues for longitudinal, mechanistic, and disease-focused studies of host-microbiome interactions in the upper GI tract.